/*
* GaussianProcessSkytrackLikelihoodParser.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evomodelxml.coalescent;
import dr.evolution.tree.Tree;
//import dr.evomodel.coalescent.GMRFSkyrideLikelihood;
import dr.evomodel.coalescent.GaussianProcessMultilocusSkytrackLikelihood;
import dr.evomodel.coalescent.GaussianProcessSkytrackLikelihood;
import dr.evomodel.tree.TreeModel;
//import dr.inference.model.MatrixParameter;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.ArrayList;
import java.util.List;
//import java.util.logging.Logger;
/**
*
*/
public class GaussianProcessSkytrackLikelihoodParser extends AbstractXMLObjectParser {
// public static final String SKYLINE_LIKELIHOOD = "gmrfSkyrideLikelihood";
public static final String SKYTRACK_LIKELIHOOD = "gpSkytrackLikelihood";
public static final String LAMBDA_BOUND_PARAMETER = "lambdaBoundParameter";
public static final String POPULATION_PARAMETER = "populationSizes";
public static final String NUMBER_POINTS="pointsParameter";
public static final String GPTYPE="GPtype";
public static final String GPCOUNTS="GPcounts";
public static final String COALFACTOR="coalfactor";
public static final String CHANGE_POINTS="changePoints";
public static final String COALCOUNT="CoalCounts";
public static final String TMRCA="timeMRCA";
// public static final String GROUP_SIZES = "groupSizes";
public static final String PRECISION_PARAMETER = "precisionParameter";
public static final String POPULATION_TREE = "populationTree";
public static final String LAMBDA_PARAMETER = "lambdaParameter";
public static final String BETA_PARAMETER = "betaParameter";
public static final String ALPHA_PARAMETER = "alphaParameter";
// public static final String COVARIATE_MATRIX = "covariateMatrix";
public static final String RANDOMIZE_TREE = "randomizeTree";
// public static final String TIME_AWARE_SMOOTHING = "timeAwareSmoothing";
public static final String RESCALE_BY_ROOT_ISSUE = "rescaleByRootHeight";
// public static final String GRID_POINTS = "gridPoints";
// public static final String OLD_SKYRIDE = "oldSkyride"; //True=No multiple loci
// public static final String NUM_GRID_POINTS = "numGridPoints";
// public static final String CUT_OFF = "cutOff";
// public static final String PHI_PARAMETER = "phiParameter";
// public static final String LATENT_PARAMETER = "latentPointParameter";
public String getParserName() {
return SKYTRACK_LIKELIHOOD;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
XMLObject cxo = xo.getChild(POPULATION_PARAMETER);
Parameter popParameter = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(PRECISION_PARAMETER);
Parameter precParameter = (Parameter) cxo.getChild(Parameter.class);
// cxo = xo.getChild(LAMBDA_BOUND_PARAMETER);
// Parameter lambda_bound = (Parameter) cxo.getChild(Parameter.class);
//
// cxo = xo.getChild(LAMBDA_PARAMETER);
// Parameter lambda_parameter = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(POPULATION_TREE);
List<Tree> treeList = new ArrayList<Tree>();
for (int i = 0; i < cxo.getChildCount(); i++) {
Object testObject = cxo.getChild(i);
if (testObject instanceof Tree) {
treeList.add((TreeModel) testObject);
}
}
// TreeModel treeModel = (TreeModel) cxo.getChild(TreeModel.class);
// cxo = xo.getChild(GROUP_SIZES);
// Parameter groupParameter = null;
// if (cxo != null) {
// groupParameter = (Parameter) cxo.getChild(Parameter.class);
//
// if (popParameter.getDimension() != groupParameter.getDimension())
// throw new XMLParseException("Population and group size parameters must have the same length");
// }
Parameter lambda_parameter;
if (xo.getChild(LAMBDA_PARAMETER) != null) {
cxo = xo.getChild(LAMBDA_PARAMETER);
lambda_parameter = (Parameter) cxo.getChild(Parameter.class);
} else {
lambda_parameter = new Parameter.Default(1.0);
}
Parameter GPtype;
if (xo.getChild(GPTYPE) != null) {
cxo = xo.getChild(GPTYPE);
GPtype = (Parameter) cxo.getChild(Parameter.class);
} else {
GPtype = new Parameter.Default(1.0);
}
Parameter Tmrca;
if (xo.getChild(TMRCA) != null) {
cxo = xo.getChild(TMRCA);
Tmrca = (Parameter) cxo.getChild(Parameter.class);
} else {
Tmrca = new Parameter.Default(1.0);
}
Parameter numPoints;
if (xo.getChild(NUMBER_POINTS) != null) {
cxo = xo.getChild(NUMBER_POINTS);
numPoints = (Parameter) cxo.getChild(Parameter.class);
} else {
numPoints = new Parameter.Default(1.0);
}
Parameter CoalCounts;
if (xo.getChild(COALCOUNT) != null) {
cxo = xo.getChild(COALCOUNT);
CoalCounts = (Parameter) cxo.getChild(Parameter.class);
} else {
CoalCounts = new Parameter.Default(1.0);
}
Parameter GPcounts;
if (xo.getChild(GPCOUNTS) != null) {
cxo = xo.getChild(GPCOUNTS);
GPcounts = (Parameter) cxo.getChild(Parameter.class);
} else {
GPcounts = new Parameter.Default(1.0);
}
Parameter coalfactor;
if (xo.getChild(COALFACTOR) != null) {
cxo = xo.getChild(COALFACTOR);
coalfactor = (Parameter) cxo.getChild(Parameter.class);
} else {
coalfactor = new Parameter.Default(1.0);
}
Parameter lambda_bound;
if (xo.getChild(LAMBDA_BOUND_PARAMETER) != null) {
cxo = xo.getChild(LAMBDA_BOUND_PARAMETER);
lambda_bound = (Parameter) cxo.getChild(Parameter.class);
} else {
lambda_bound = new Parameter.Default(1.0);
}
Parameter alpha_parameter;
if (xo.getChild(ALPHA_PARAMETER) != null) {
cxo = xo.getChild(ALPHA_PARAMETER);
alpha_parameter = (Parameter) cxo.getChild(Parameter.class);
} else {
alpha_parameter = new Parameter.Default(0.001);
}
Parameter beta_parameter;
if (xo.getChild(BETA_PARAMETER) != null) {
cxo = xo.getChild(BETA_PARAMETER);
beta_parameter = (Parameter) cxo.getChild(Parameter.class);
} else {
beta_parameter = new Parameter.Default(0.001);
}
Parameter change_points;
if (xo.getChild(CHANGE_POINTS) != null) {
cxo = xo.getChild(CHANGE_POINTS);
change_points = (Parameter) cxo.getChild(Parameter.class);
} else {
change_points = new Parameter.Default(0,1);
}
/*
Parameter gridPoints = null;
if (xo.getChild(GRID_POINTS) != null) {
cxo = xo.getChild(GRID_POINTS);
gridPoints = (Parameter) cxo.getChild(Parameter.class);
}
*/
// Parameter numGridPoints = new Parameter.Default(0,1);
// if (xo.getChild(NUM_GRID_POINTS) != null) {
// cxo = xo.getChild(NUM_GRID_POINTS);
// numGridPoints = (Parameter) cxo.getChild(Parameter.class);
// }
// Parameter cutOff = null;
// if (xo.getChild(CUT_OFF) != null) {
// cxo = xo.getChild(CUT_OFF);
// cutOff = (Parameter) cxo.getChild(Parameter.class);
// }
//
// Parameter phi = null;
// if (xo.getChild(PHI_PARAMETER) != null) {
// cxo = xo.getChild(PHI_PARAMETER);
// phi = (Parameter) cxo.getChild(Parameter.class);
// }
//
//
// Parameter beta = null;
// if (xo.getChild(BETA_PARAMETER) != null) {
// cxo = xo.getChild(BETA_PARAMETER);
// beta = (Parameter) cxo.getChild(Parameter.class);
// }
// MatrixParameter dMatrix = null;
// if (xo.getChild(COVARIATE_MATRIX) != null) {
// cxo = xo.getChild(COVARIATE_MATRIX);
// dMatrix = (MatrixParameter) cxo.getChild(MatrixParameter.class);
// }
// boolean timeAwareSmoothing = GMRFSkyrideLikelihood.TIME_AWARE_IS_ON_BY_DEFAULT;
// if (xo.hasAttribute(TIME_AWARE_SMOOTHING)) {
// timeAwareSmoothing = xo.getBooleanAttribute(TIME_AWARE_SMOOTHING);
// }
// if ((dMatrix != null && beta == null) || (dMatrix == null && beta != null))
// throw new XMLParseException("Must specify both a set of regression coefficients and a design matrix.");
//
// if (dMatrix != null) {
// if (dMatrix.getRowDimension() != popParameter.getDimension())
// throw new XMLParseException("Design matrix row dimension must equal the population parameter length.");
// if (dMatrix.getColumnDimension() != beta.getDimension())
// throw new XMLParseException("Design matrix column dimension must equal the regression coefficient length.");
// }
if (xo.getAttribute(RANDOMIZE_TREE, false)) {
for (Tree tree : treeList) {
if (tree instanceof TreeModel) {
GaussianProcessSkytrackLikelihood.checkTree((TreeModel) tree);
} else {
throw new XMLParseException("Can not randomize a fixed tree");
}
}
}
// XMLObject latentChild = xo.getChild(LATENT_PARAMETER);
// Parameter latentPoints = (Parameter) latentChild.getChild(Parameter.class);
boolean rescaleByRootHeight = xo.getAttribute(RESCALE_BY_ROOT_ISSUE, true);
// Logger.getLogger("dr.evomodel").info("The " + SKYTRACK_LIKELIHOOD + " has " +
// (timeAwareSmoothing ? "time aware smoothing" : "uniform smoothing"));
if (treeList.size()==1) {
return new GaussianProcessSkytrackLikelihood(treeList, precParameter,
rescaleByRootHeight, lambda_bound, lambda_parameter, popParameter,alpha_parameter,beta_parameter, change_points,
GPtype, GPcounts, coalfactor, CoalCounts, numPoints,Tmrca);
} else {
return new GaussianProcessMultilocusSkytrackLikelihood(treeList, precParameter, rescaleByRootHeight, lambda_bound,
lambda_parameter, popParameter, alpha_parameter, beta_parameter, change_points, GPtype,GPcounts,coalfactor, CoalCounts, numPoints,Tmrca);
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element represents the likelihood of the tree given the population size vector.";
}
public Class getReturnType() {
return GaussianProcessSkytrackLikelihood.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(POPULATION_PARAMETER, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}),
new ElementRule(CHANGE_POINTS, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}),
new ElementRule(PRECISION_PARAMETER, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}),
new ElementRule(LAMBDA_BOUND_PARAMETER, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}),
new ElementRule(LAMBDA_PARAMETER, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}),
new ElementRule(ALPHA_PARAMETER, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}),
new ElementRule(BETA_PARAMETER, new XMLSyntaxRule[]{
new ElementRule(Parameter.class)
}),
// new ElementRule(PHI_PARAMETER, new XMLSyntaxRule[]{
// new ElementRule(Parameter.class)
// }, true), // Optional
new ElementRule(POPULATION_TREE, new XMLSyntaxRule[]{
new ElementRule(TreeModel.class, 1, Integer.MAX_VALUE)
}),
// new ElementRule(GROUP_SIZES, new XMLSyntaxRule[]{
// new ElementRule(Parameter.class)
// }, true),
// new ElementRule(LATENT_PARAMETER,Parameter.class),
AttributeRule.newBooleanRule(RESCALE_BY_ROOT_ISSUE, true),
AttributeRule.newBooleanRule(RANDOMIZE_TREE, true),
// AttributeRule.newBooleanRule(TIME_AWARE_SMOOTHING, true),
// AttributeRule.newBooleanRule(OLD_SKYRIDE, true)
};
}